[gmx-users] Temperature or Pressure Coupling

[sun]

Hello 
I want to simulate a protein in water and observe its behavior alone and then 
in the presence of ligand. I have read somewhere that NPT MD is best for 
pro-lig complexes as it resembles the in vitro and in vivo conditions 
(conformational changes,biomolecular reactions, binding etc.). So My question 
is whether I should use NpTMD for protein alone as well? Or if anyone could 
give some good reference.
Regards
Suniba

Sent from my iPhone
Sent from my iPhone
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] How to get an index file containing non polar atoms in gromacs?

[Catarina A. Carvalheda dos Santos]

I think you can figure this out after playing 5 min with the make_ndx tool,
but here it goes:

"r ILE | r LEU | r VAL" will select all the isoleucines, leucines and
valines in your system.

Cheers,


On 25 January 2016 at 12:23, Shima ebrahimi  wrote:

>
>
> Dear Users,
>
> I want to determine hydrophobic interaction between ligand and protein
> using g_mindist. However, how can I identify non-polar atoms and specify
> them in the index file.Could anyone help me?
> Regards,
> Shima
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>



-- 
Catarina A. Carvalheda

PhD Student
Computational Biology Division
SSE & SLS
University of Dundee
DD1 5EH, Dundee, Scotland, UK
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Error in comparison of Coulomb-14 potential?

[Andreas Mecklenfeld]

Dear all,

I want to perform an alchemical change of state of a molecule in TIP3P, 
where I do only change the partial charges of the atomtypes. To control 
my results, I perform two MD runs with the different charge sets 
respectively.


I'm interested in the Coulomb-14 interactions of the solute (since TIP3P 
has none obviously) and would have expected that the potentials of the 
end states match those of the classic runs.


For the classic MD, topology A results in -5.74e+02 kJ/mol, while for B 
it's -9.04e+02 kJ/mol which seems reasonable.
However, the Coulomb-14 potential of alchemical state A (lambda = 0) is 
-5.74e+02 kJ/mol and for state B (lambda = 1)  it's -5.69e+02 kJ/mol.


I would have expected that the topology of the alchemical end state B 
matches topology B of the MD run, since all parameters should be the 
same. The results are the averages given in the log-files.


Are my considerations wrong or could this be a bug in Gromacs?

Thanks,
Andreas


--
M. Sc. Andreas Mecklenfeld
Stipendiat

Technische Universität Braunschweig
Institut für Thermodynamik
Hans-Sommer-Straße 5
38106 Braunschweig
Deutschland / Germany

Tel: +49 (0)531 391-2634
Fax: +49 (0)531 391-7814

http://www.ift-bs.de

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Gromos96 53a6 and Berger Lipids

[Kindlein, Moritz]

Hi all,

I would appreciate your opinion on a quite often discussed topic.

I am doing simulations of triglycerides and phosphoglycerides, and I am 
currently using the combination of gromos96 53a6 and Berger Lipid parameters as 
suggested in Justin Lemkuls Tutorial.
If I am right, this combination has been shown to fail to reproduce the 
experimental parameters of DPPC membranes to satisfactory accuracy quite a 
while ago. F.e. see the following papers:
Kukol 2009:10.1021/ct8003468
Chandrasekhar et al. 2005: 10.1080/08927020500134243

So my question are:

1.   The gromos96 53a6 and Berger Lipid combination is still used in the 
tutorial, so I am wondering if there are any newer validations for this 
combination, which I am missing? How would you decide if this is a valid 
combination?

2.   Is there a similar tutorial (like KALP-15) which shows how to set up 
the gromos96 53a6 and Kukol combination? Or do I only have to include the .itp 
files of the Kukol-paper (see above) in my topology?

Any answers are appreciated very much:)! I hope I didn't miss some already 
existing answers in the mailing list.

Best regards,
Moritz



-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Error - syntax

[Chang Woon Jang]

Dear Mark,

   Thank you for the information. I have changed the topol.top file now like

I put another three lined for posres right below each itp, DGA.itp and
J230.itp.

; Include forcefield parameters
;#include "forcefield.itp"

; Include chain topologies
#include "DGA.itp"
#ifdef POSRES
#include "porse_A.itp"
#endif

#include "J230.itp"
#ifdef POSRES
#include "porse_B.itp"
#endif

[ system ]
; Name
Built with Packmol

[ molecules ]
; Compound#mols
Other_chain_A   200
Other_chain_B   100


   In the DGA.itp file,

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
  1 1   no  0.0 0.0

[ atomtypes ]
;typemasscharge   ptype  sigma  epsilon
 B 42.080999  0.000   A1.0  1.0
 A 151.18579  0.000   A1.0  1.0

[ moleculetype ]
Other_chain_A 3

[atoms]
; nr type resnr residue atom cgnr charge mass
1 A 1 RES A1 1 0.00 151.18579
2 A 1 RES A2 2 0.00 151.18579
3 B 1 RES B1 3 0.00 42.080999


[ bonds ]
1 3   8   1 1.0; 1:bond:1
2 3   8   1 1.0; 1:bond:2

[ angles ]
1 3 2   8  1 1.0  ; 1:angle:1



In J230.itp file,

[ atomtypes ]
;typemasscharge   ptype  sigma  epsilon
 D 100.16139  0.000   A1.0  1.0
 C 74.103099  0.000   A1.0  1.0

[ moleculetype ]
Other_chain_B 3

[atoms]
; nr type resnr residue atom cgnr charge mass
1 C 1 RES C1 1 0.00 74.103099
2 D 1 RES D1 2 0.00 100.16139
3 C 1 RES C2 3 0.00 74.103099


[ bonds ]
1 2   8  1  1.0  ; 1:bond:1
2 3   8  1  1.0  ; 1:bond:2

[ angles ]
1 2 3   8   1  1.0 ; 1:angle:1


The error still occurred as follow.

---
Program gmx, VERSION 5.0.8-dev-20151014-1f04b58
Source code file:
/home/chang/PACKAGE/votca/src/gromacs/src/gromacs/gmxpreprocess/topio.c,
line: 727

Fatal error:
Syntax error - File J230.topfile.itp, line 5
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---


Don't I understand the passage correctly you linked?

Thank you.

Best regards,
Changwoon Jang




On Mon, Jan 25, 2016 at 1:34 PM, Mark Abraham 
wrote:

> Hi,
>
> See
> http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_xxx
>
> Mark
>
> On Mon, 25 Jan 2016 19:19 Chang Woon Jang  wrote:
>
> > Dear Gromacs Users,
> >
> >  I have two types of molecules. The topology file was separated by one
> > (topol.top) and two (DGA.itp, and J230.itp).
> >
> > The format I made in topol.top is
> >
> > #include "DGA.itp"
> > #include "J230.itp"
> >
> > [ system ]
> > ; Name
> > DGA and J230
> >
> > [ molecules ]
> > ; Compound#mols
> > Other_chain_A  200
> > Other_chain_B  100
> >
> > In the DGA.itp and J230.itp files, I formatted like but only difference
> > between DGA.itp and J230.tip is type (C and D) and mass.
> >
> >
> > [ defaults ]
> > ; nbfunccomb-rule   gen-pairsfudgeLJ  fudgeQQ
> >   1 1 no   0.0 0.0
> > [ atomtypes ]
> > ; typemass   charge ptype sigma   epsilon
> >  B 42.0909990.000  A1. 1.
> >  A 151.185798  0.000  A1. 1.
> >
> > [ molecuetype ]
> > Other_chain_A 3
> >
> > [atoms]
> > ; nr type resnr residue atom cgnr charge mass
> > 1 A 1 RES A1 1 0.0 151.185798
> > 2 A 1 RES A2 2 0.0 151.185798
> > 3 B 1 RES B1 3 0.0 42.080999
> >
> > [ bonds ]
> > 1 38   1   1.0 ; 1:bond:1
> > 2 38   1   1.0 ; 1:bond:2
> >
> > [ angles ]
> > 1 3 2   8   1  1.0; 1:angle:1
> >
> > An error says,
> >
> > Fatal error:
> > Syntax error - file DGA.itp, line 1
> > Last line read:
> > ' [ defaults ]'
> > invalid order for directive moleculetype
> > For more .
> >
> >
> > I am trying to simulate a Coarse-grained model and the topology file was
> > created. I think that the formatting is correct following an example from
> > votca coarse graining tool. When I use two type of molecules in atomistic
> > scale, these separated topology files work fine.
> >
> > Would you please what the correct format of this to be run?
> >
> > Thank you very much for your advise.
> >
> >
> > Best regards,
> > Changwoon Jang,
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> 

Re: [gmx-users] Temperature Annealing

[Justin Lemkul]

On 1/25/16 2:41 PM, abdus sabuj wrote:

Hi Justin,

Here is the mdp file I used for NPT equilibration...


integrator   = md
nsteps   = 1000
dt   = 0.001
nstenergy= 1000
nstxout  = 1000
nstvout  = 1000





vdw-type = cut-off


continuation= yes; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H
bonds) constrained
;lincs_iter  = 1 ; accuracy of LINCS
;lincs_order = 4 ; also related to accuracy
lincs-warnangle = 90; warning after rotating the bond


ns_type = grid  ; search neighboring grid cels
nstlist = 10 ; 10 fs
rlist   = 1.4   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.4   ; short-range electrostatic cutoff (in nm)
rvdw= 1.4   ; short-range van der Waals cutoff (in nm)
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT

; set temperature to 300K
tcoupl   = v-rescale
tc-grps  = system
tau-t= 0.1
ref-t= 300
; and pressure to 1 bar
pcoupl   = berendsen
ref-p= 1
compressibility  = 4.5e-5
tau-p= 5
; generate initial velocities
gen-vel  = no
;gen-temp = 300
;gen_seed= -1
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme

; COM motion removal
; These options remove motion of the protein/bilayer relative to the
solvent/ions
nstcomm = 1
comm-mode   = Linear
comm-grps   = system

...


And for Production run, I am using the mdp file as below


integrator   = md
nsteps   =1000
dt   = 0.001
nstenergy= 1000
nstxout  = 1000
nstvout  = 1000


vdw-type = cut-off

continuation= yes; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H
bonds) constrained
;lincs_iter  = 1 ; accuracy of LINCS
;lincs_order = 8 ; also related to accuracy
lincs-warnangle = 90; warning after rotating the bond


ns_type = grid  ; search neighboring grid cels
nstlist = 10 ; 10 fs
rlist   = 1.4   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.4   ; short-range electrostatic cutoff (in nm)
rvdw= 1.4   ; short-range van der Waals cutoff (in nm)

coulombtype =PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT

; set temperature to 300K
tcoupl   = Nose-Hoover
tc-grps  = system
tau-t= 0.2
ref-t= 300
; and pressure to 1 bar
pcoupl   = Parrinello-Rahman
ref-p= 1
compressibility  = 4.5e-5
tau-p= 5
pcoupltype  = isotropic
; generate initial velocities
gen-vel  = no
;gen-temp = 300
;gen_seed= -1
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres ; account for cut-off vdW scheme

;simulated anneling
annealing = single
annealing-npoints = 6
annealing-time= 0 2000 4000 6000 8000 1
annealing-temp= 300 310 320 330 340 350

; COM motion removal
; These options remove motion of the protein/bilayer relative to the
solvent/ions
nstcomm = 1
comm-mode   = linear
comm-grps   = system
cos-acceleration = 0.01


...



And does your grompp invocation correctly pass the equilibration checkpoint when 
preparing the production .tpr file?  This is why I asked for commands, too.


-Justin


Thanks,
Sabuj


On Mon, Jan 25, 2016 at 12:54 PM, Justin Lemkul  wrote:




On 1/25/16 1:51 PM, abdus sabuj wrote:


Hi Mark,
I have equilibrated my system very well before the production run at 300K,
but at time zero, the temperature is at 321K.

Here is the fluctuations I am getting.

time (ns)  

Re: [gmx-users] Error - syntax

[Justin Lemkul]

On 1/25/16 2:50 PM, Chang Woon Jang wrote:

Dear Mark,

Thank you for the information. I have changed the topol.top file now like

I put another three lined for posres right below each itp, DGA.itp and
J230.itp.

; Include forcefield parameters
;#include "forcefield.itp"

; Include chain topologies
#include "DGA.itp"
#ifdef POSRES
#include "porse_A.itp"
#endif

#include "J230.itp"
#ifdef POSRES
#include "porse_B.itp"
#endif

[ system ]
; Name
Built with Packmol

[ molecules ]
; Compound#mols
Other_chain_A   200
Other_chain_B   100


In the DGA.itp file,

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
   1 1   no  0.0 0.0

[ atomtypes ]
;typemasscharge   ptype  sigma  epsilon
  B 42.080999  0.000   A1.0  1.0
  A 151.18579  0.000   A1.0  1.0

[ moleculetype ]
Other_chain_A 3

[atoms]
; nr type resnr residue atom cgnr charge mass
1 A 1 RES A1 1 0.00 151.18579
2 A 1 RES A2 2 0.00 151.18579
3 B 1 RES B1 3 0.00 42.080999


[ bonds ]
1 3   8   1 1.0; 1:bond:1
2 3   8   1 1.0; 1:bond:2

[ angles ]
1 3 2   8  1 1.0  ; 1:angle:1



In J230.itp file,

[ atomtypes ]
;typemasscharge   ptype  sigma  epsilon
  D 100.16139  0.000   A1.0  1.0
  C 74.103099  0.000   A1.0  1.0

[ moleculetype ]
Other_chain_B 3

[atoms]
; nr type resnr residue atom cgnr charge mass
1 C 1 RES C1 1 0.00 74.103099
2 D 1 RES D1 2 0.00 100.16139
3 C 1 RES C2 3 0.00 74.103099


[ bonds ]
1 2   8  1  1.0  ; 1:bond:1
2 3   8  1  1.0  ; 1:bond:2

[ angles ]
1 2 3   8   1  1.0 ; 1:angle:1


The error still occurred as follow.

---
Program gmx, VERSION 5.0.8-dev-20151014-1f04b58
Source code file:
/home/chang/PACKAGE/votca/src/gromacs/src/gromacs/gmxpreprocess/topio.c,
line: 727

Fatal error:
Syntax error - File J230.topfile.itp, line 5
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---


Don't I understand the passage correctly you linked?



Spend some time reading Chapter 5 of the manual.  You have to declare all force 
field-level directives before you can declare molecule-level directives.  The 
parser has to know everything about the form of the force field before you can 
start building molecules within that force field.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Changing a quantity at each time step using a formula

[AshutoshAkshay Shah]

Hello GROMACS users,

I am simulating a graphene based supercapacitor. I want to change the
charge of each particle at the electrode surface such that the voltage of
the electrochemical cell remains constant. I know the formula to be used
for this, but I have no idea how to implement it. I want to know where to
write the code (if required) and in which file.
Thanks!
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Temperature Annealing

[abdus sabuj]

Hi Justin,

Here is the mdp file I used for NPT equilibration...


integrator   = md
nsteps   = 1000
dt   = 0.001
nstenergy= 1000
nstxout  = 1000
nstvout  = 1000





vdw-type = cut-off


continuation= yes; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H
bonds) constrained
;lincs_iter  = 1 ; accuracy of LINCS
;lincs_order = 4 ; also related to accuracy
lincs-warnangle = 90; warning after rotating the bond


ns_type = grid  ; search neighboring grid cels
nstlist = 10 ; 10 fs
rlist   = 1.4   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.4   ; short-range electrostatic cutoff (in nm)
rvdw= 1.4   ; short-range van der Waals cutoff (in nm)
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT

; set temperature to 300K
tcoupl   = v-rescale
tc-grps  = system
tau-t= 0.1
ref-t= 300
; and pressure to 1 bar
pcoupl   = berendsen
ref-p= 1
compressibility  = 4.5e-5
tau-p= 5
; generate initial velocities
gen-vel  = no
;gen-temp = 300
;gen_seed= -1
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme

; COM motion removal
; These options remove motion of the protein/bilayer relative to the
solvent/ions
nstcomm = 1
comm-mode   = Linear
comm-grps   = system

...


And for Production run, I am using the mdp file as below


integrator   = md
nsteps   =1000
dt   = 0.001
nstenergy= 1000
nstxout  = 1000
nstvout  = 1000


vdw-type = cut-off

continuation= yes; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H
bonds) constrained
;lincs_iter  = 1 ; accuracy of LINCS
;lincs_order = 8 ; also related to accuracy
lincs-warnangle = 90; warning after rotating the bond


ns_type = grid  ; search neighboring grid cels
nstlist = 10 ; 10 fs
rlist   = 1.4   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.4   ; short-range electrostatic cutoff (in nm)
rvdw= 1.4   ; short-range van der Waals cutoff (in nm)

coulombtype =PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT

; set temperature to 300K
tcoupl   = Nose-Hoover
tc-grps  = system
tau-t= 0.2
ref-t= 300
; and pressure to 1 bar
pcoupl   = Parrinello-Rahman
ref-p= 1
compressibility  = 4.5e-5
tau-p= 5
pcoupltype  = isotropic
; generate initial velocities
gen-vel  = no
;gen-temp = 300
;gen_seed= -1
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres ; account for cut-off vdW scheme

;simulated anneling
annealing = single
annealing-npoints = 6
annealing-time= 0 2000 4000 6000 8000 1
annealing-temp= 300 310 320 330 340 350

; COM motion removal
; These options remove motion of the protein/bilayer relative to the
solvent/ions
nstcomm = 1
comm-mode   = linear
comm-grps   = system
cos-acceleration = 0.01


...

Thanks,
Sabuj


On Mon, Jan 25, 2016 at 12:54 PM, Justin Lemkul  wrote:

>
>
> On 1/25/16 1:51 PM, abdus sabuj wrote:
>
>> Hi Mark,
>> I have equilibrated my system very well before the production run at 300K,
>> but at time zero, the temperature is at 321K.
>>
>> Here is the fluctuations I am getting.
>>
>> time (ns)  temperature (K)
>> 0  321
>> 2  315
>> 4   333
>> 6   358
>> 8   377
>> 10 397
>>
>>
> Please provide 

Re: [gmx-users] Gromos96 53a6 and Berger Lipids

[Piggot T.]

Hi,

Neither of the two papers you mentioned use the Berger lipid parameters, rather 
they both use purely GROMOS lipid force fields. This is plain GROMOS 45A3 for 
the Chandrasekhar et al. paper (using older, original, GROMOS DPPC lipid 
charges). This force field doesn't reproduce the properties of DPPC well and 
will rapidly enter a gel phase unless you use a surface tension or fixed box 
size (which is not recommended). In the case of the Kukol work, this is a 
modified 53A6 force field with the QM charges of Chiu et al. (the same charges 
used in the Berger lipids and in the vast majority of other united-atom PC 
lipid force fields) and a larger van der Waals radius (atom type CH0) for the 
carbonyl carbons (as originally suggested in another paper by Chandrasekhar et 
al.). With both the increase in van der Waals radius and change in charges, 
DPPC membranes behave fairly well when compared to experimental determined 
membrane properties. I would note, however, that there are issues wit
 h some of the other lipid parameters provided in the Kukol paper (POPC/POPG 
parameters). If you care about this, I can point you to some papers for more 
details. As for your question, if you wish to use these parameters you are 
correct that all you need to do is to include the itp files in your topology. 

If you are just simulating membranes, you don't need to worry about the 
combination of the Berger parameters with anything else (well, apart from 
water/ions, etc.). With the Berger lipids, people typically talk about 
combining them with protein force fields (GROMOS/OPLS/AMBER ones) when they are 
wanting to do membrane and protein simulations, as is the case in the tutorial 
(note, combining different force fields is generally not a good thing to do, 
but due to the mix of parameters that make up the Berger lipids it has shown to 
be acceptable in this case). As for whether the Berger lipid parameters 
reproduce the experimental properties of DPPC membranes, there are numerous 
publications out there on this. In general, Berger DPPC membranes behave ok but 
there are probably better lipid force fields available. If you move beyond 
phosphatidylcholine lipids, the Berger parameters don't tend to behave well for 
other types of phospholipids (again, there are lots of publications out th
 ere regarding this).

Hopefully this makes things a bit clearer.

Cheers

Tom


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Kindlein, 
Moritz [moritz.kindl...@tum.de]
Sent: 25 January 2016 14:02
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Gromos96 53a6 and Berger Lipids

Hi all,

I would appreciate your opinion on a quite often discussed topic.

I am doing simulations of triglycerides and phosphoglycerides, and I am 
currently using the combination of gromos96 53a6 and Berger Lipid parameters as 
suggested in Justin Lemkuls Tutorial.
If I am right, this combination has been shown to fail to reproduce the 
experimental parameters of DPPC membranes to satisfactory accuracy quite a 
while ago. F.e. see the following papers:
Kukol 2009:10.1021/ct8003468
Chandrasekhar et al. 2005: 10.1080/08927020500134243

So my question are:

1.   The gromos96 53a6 and Berger Lipid combination is still used in the 
tutorial, so I am wondering if there are any newer validations for this 
combination, which I am missing? How would you decide if this is a valid 
combination?

2.   Is there a similar tutorial (like KALP-15) which shows how to set up 
the gromos96 53a6 and Kukol combination? Or do I only have to include the .itp 
files of the Kukol-paper (see above) in my topology?

Any answers are appreciated very much:)! I hope I didn't miss some already 
existing answers in the mailing list.

Best regards,
Moritz



--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Build fails with AVX2_256 on Intel Xeon CPU E5-2680 v3

[Nicolas Cheron]

Hi,

All my installations are made from a clean build directory. I am
using CentOS release 6.6 and the CPU is Intel Xeon CPU E5-2650 v3 @
2.30GHz. Here is the exact list of command that I have used (as I said, I
have also tried with gcc4.9.3 and gcc5.2):

module purge
module load gcc/4.8.5
cd /home2/ncheron/Programs/
cp 00-Install/gromacs-5.1.1.tar.gz .
tar zxf gromacs-5.1.1.tar.gz
rm gromacs-5.1.1.tar.gz
cd /home2/ncheron/Programs/gromacs-5.1.1
umask 022
mkdir build
cd /home2/ncheron/Programs/gromacs-5.1.1/build
mkdir /home2/ncheron/Programs/Gromacs5.1.1
CMAKE_PREFIX_PATH=/home2/ncheron/Programs/LibXml_2.9.2:/home2/ncheron/Programs/Boost_1.60.0
cmake .. -DGMX_OPENMP=ON -DGMX_THREAD_MPI=ON -DGMX_MPI=OFF -DGMX_GPU=OFF
-DGMX_DOUBLE=OFF -DGMX_BUILD_MDRUN_ONLY=ON
-DCMAKE_INSTALL_PREFIX=/home2/ncheron/Programs/Gromacs5.1.1
-DGMX_BUILD_OWN_FFTW=ON
-DGMX_BUILD_OWN_FFTW_URL=/home2/ncheron/Programs/00-Install/fftw-3.3.4.tar.gz
-DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_Dell -DGMX_LIBS_SUFFIX=_Dell
-DGMX_SIMD=AVX2_256
make -j4
make install

The error file says:
CMake Error at cmake/gmxManageSimd.cmake:271 (message):
  Cannot find AVX2 compiler flag.  Use a newer compiler, or choose AVX SIMD
  (slower).
Call Stack (most recent call first):
  CMakeLists.txt:645 (gmx_manage_simd)


The output file says:
-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- Check for working C compiler: /usr/local/gcc/4.8.5/bin/gcc
-- Check for working C compiler: /usr/local/gcc/4.8.5/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/local/gcc/4.8.5/bin/g++
-- Check for working CXX compiler: /usr/local/gcc/4.8.5/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp
-- Performing Test CFLAGS_WARN
-- Performing Test CFLAGS_WARN - Success
-- Performing Test CFLAGS_WARN_EXTRA
-- Performing Test CFLAGS_WARN_EXTRA - Success
-- Performing Test CFLAGS_WARN_UNDEF
-- Performing Test CFLAGS_WARN_UNDEF - Success
-- Performing Test CFLAGS_WARN_REL
-- Performing Test CFLAGS_WARN_REL - Success
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_WARN
-- Performing Test CXXFLAGS_WARN - Success
-- Performing Test CXXFLAGS_WARN_EXTRA
-- Performing Test CXXFLAGS_WARN_EXTRA - Success
-- Performing Test CXXFLAGS_WARN_UNDEF
-- Performing Test CXXFLAGS_WARN_UNDEF - Success
-- Performing Test CXXFLAGS_WARN_REL
-- Performing Test CXXFLAGS_WARN_REL - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file regex.h
-- Looking for include file regex.h - found
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Looking for _aligned_malloc
-- Looking for _aligned_malloc - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Looking for rsqrt
-- Looking for rsqrt - not found
-- Looking for rsqrtf
-- Looking for rsqrtf - not found
-- Looking for sqrtf
-- Looking for sqrtf - found
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found

[gmx-users] Temperature Annealing

[abdus sabuj]

Dear gmx users,

I am trying to get viscosity as a function of temperature. So I have put
the following annealing inputs to the mdp file.

;simulated anneling
annealing = single
annealing-npoints = 6
annealing-time= 0 2000 4000 6000 8000 1
annealing-temp= 300 310 320 330 340 350

i.e, at 10ns, the temperature should be at 350K, right? But I saw after my
npt simulation that, the last temperature reached at 400K. Why that's
happening, did I make any mistakes?

Thanks,
Sabuj
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Error - syntax

[Mark Abraham]

Hi,

See
http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_xxx

Mark

On Mon, 25 Jan 2016 19:19 Chang Woon Jang  wrote:

> Dear Gromacs Users,
>
>  I have two types of molecules. The topology file was separated by one
> (topol.top) and two (DGA.itp, and J230.itp).
>
> The format I made in topol.top is
>
> #include "DGA.itp"
> #include "J230.itp"
>
> [ system ]
> ; Name
> DGA and J230
>
> [ molecules ]
> ; Compound#mols
> Other_chain_A  200
> Other_chain_B  100
>
> In the DGA.itp and J230.itp files, I formatted like but only difference
> between DGA.itp and J230.tip is type (C and D) and mass.
>
>
> [ defaults ]
> ; nbfunccomb-rule   gen-pairsfudgeLJ  fudgeQQ
>   1 1 no   0.0 0.0
> [ atomtypes ]
> ; typemass   charge ptype sigma   epsilon
>  B 42.0909990.000  A1. 1.
>  A 151.185798  0.000  A1. 1.
>
> [ molecuetype ]
> Other_chain_A 3
>
> [atoms]
> ; nr type resnr residue atom cgnr charge mass
> 1 A 1 RES A1 1 0.0 151.185798
> 2 A 1 RES A2 2 0.0 151.185798
> 3 B 1 RES B1 3 0.0 42.080999
>
> [ bonds ]
> 1 38   1   1.0 ; 1:bond:1
> 2 38   1   1.0 ; 1:bond:2
>
> [ angles ]
> 1 3 2   8   1  1.0; 1:angle:1
>
> An error says,
>
> Fatal error:
> Syntax error - file DGA.itp, line 1
> Last line read:
> ' [ defaults ]'
> invalid order for directive moleculetype
> For more .
>
>
> I am trying to simulate a Coarse-grained model and the topology file was
> created. I think that the formatting is correct following an example from
> votca coarse graining tool. When I use two type of molecules in atomistic
> scale, these separated topology files work fine.
>
> Would you please what the correct format of this to be run?
>
> Thank you very much for your advise.
>
>
> Best regards,
> Changwoon Jang,
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Build fails with AVX2_256 on Intel Xeon CPU E5-2680 v3

[Mark Abraham]

Hi,

Thanks. Indications are that you also need an updated binaries package.
Specifically, there's a test that the compiler accepts the avx2 flag, which
is passing. But some other part of the infrastructure isn't working
(probably the linker) because the next test fails.

Mark

On Mon, 25 Jan 2016 18:57 Nicolas Cheron 
wrote:

> Hi,
>
> All my installations are made from a clean build directory. I am
> using CentOS release 6.6 and the CPU is Intel Xeon CPU E5-2650 v3 @
> 2.30GHz. Here is the exact list of command that I have used (as I said, I
> have also tried with gcc4.9.3 and gcc5.2):
>
> module purge
> module load gcc/4.8.5
> cd /home2/ncheron/Programs/
> cp 00-Install/gromacs-5.1.1.tar.gz .
> tar zxf gromacs-5.1.1.tar.gz
> rm gromacs-5.1.1.tar.gz
> cd /home2/ncheron/Programs/gromacs-5.1.1
> umask 022
> mkdir build
> cd /home2/ncheron/Programs/gromacs-5.1.1/build
> mkdir /home2/ncheron/Programs/Gromacs5.1.1
>
> CMAKE_PREFIX_PATH=/home2/ncheron/Programs/LibXml_2.9.2:/home2/ncheron/Programs/Boost_1.60.0
> cmake .. -DGMX_OPENMP=ON -DGMX_THREAD_MPI=ON -DGMX_MPI=OFF -DGMX_GPU=OFF
> -DGMX_DOUBLE=OFF -DGMX_BUILD_MDRUN_ONLY=ON
> -DCMAKE_INSTALL_PREFIX=/home2/ncheron/Programs/Gromacs5.1.1
> -DGMX_BUILD_OWN_FFTW=ON
>
> -DGMX_BUILD_OWN_FFTW_URL=/home2/ncheron/Programs/00-Install/fftw-3.3.4.tar.gz
> -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_Dell -DGMX_LIBS_SUFFIX=_Dell
> -DGMX_SIMD=AVX2_256
> make -j4
> make install
>
> The error file says:
> CMake Error at cmake/gmxManageSimd.cmake:271 (message):
>   Cannot find AVX2 compiler flag.  Use a newer compiler, or choose AVX SIMD
>   (slower).
> Call Stack (most recent call first):
>   CMakeLists.txt:645 (gmx_manage_simd)
>
>
> The output file says:
> -- The C compiler identification is GNU 4.8.5
> -- The CXX compiler identification is GNU 4.8.5
> -- Check for working C compiler: /usr/local/gcc/4.8.5/bin/gcc
> -- Check for working C compiler: /usr/local/gcc/4.8.5/bin/gcc -- works
> -- Detecting C compiler ABI info
> -- Detecting C compiler ABI info - done
> -- Detecting C compile features
> -- Detecting C compile features - done
> -- Check for working CXX compiler: /usr/local/gcc/4.8.5/bin/g++
> -- Check for working CXX compiler: /usr/local/gcc/4.8.5/bin/g++ -- works
> -- Detecting CXX compiler ABI info
> -- Detecting CXX compiler ABI info - done
> -- Detecting CXX compile features
> -- Detecting CXX compile features - done
> -- Try OpenMP C flag = [-fopenmp]
> -- Performing Test OpenMP_FLAG_DETECTED
> -- Performing Test OpenMP_FLAG_DETECTED - Success
> -- Try OpenMP CXX flag = [-fopenmp]
> -- Performing Test OpenMP_FLAG_DETECTED
> -- Performing Test OpenMP_FLAG_DETECTED - Success
> -- Found OpenMP: -fopenmp
> -- Performing Test CFLAGS_WARN
> -- Performing Test CFLAGS_WARN - Success
> -- Performing Test CFLAGS_WARN_EXTRA
> -- Performing Test CFLAGS_WARN_EXTRA - Success
> -- Performing Test CFLAGS_WARN_UNDEF
> -- Performing Test CFLAGS_WARN_UNDEF - Success
> -- Performing Test CFLAGS_WARN_REL
> -- Performing Test CFLAGS_WARN_REL - Success
> -- Performing Test CFLAGS_EXCESS_PREC
> -- Performing Test CFLAGS_EXCESS_PREC - Success
> -- Performing Test CFLAGS_COPT
> -- Performing Test CFLAGS_COPT - Success
> -- Performing Test CFLAGS_NOINLINE
> -- Performing Test CFLAGS_NOINLINE - Success
> -- Performing Test CXXFLAGS_WARN
> -- Performing Test CXXFLAGS_WARN - Success
> -- Performing Test CXXFLAGS_WARN_EXTRA
> -- Performing Test CXXFLAGS_WARN_EXTRA - Success
> -- Performing Test CXXFLAGS_WARN_UNDEF
> -- Performing Test CXXFLAGS_WARN_UNDEF - Success
> -- Performing Test CXXFLAGS_WARN_REL
> -- Performing Test CXXFLAGS_WARN_REL - Success
> -- Performing Test CXXFLAGS_EXCESS_PREC
> -- Performing Test CXXFLAGS_EXCESS_PREC - Success
> -- Performing Test CXXFLAGS_COPT
> -- Performing Test CXXFLAGS_COPT - Success
> -- Performing Test CXXFLAGS_NOINLINE
> -- Performing Test CXXFLAGS_NOINLINE - Success
> -- Looking for include file unistd.h
> -- Looking for include file unistd.h - found
> -- Looking for include file pwd.h
> -- Looking for include file pwd.h - found
> -- Looking for include file dirent.h
> -- Looking for include file dirent.h - found
> -- Looking for include file time.h
> -- Looking for include file time.h - found
> -- Looking for include file sys/time.h
> -- Looking for include file sys/time.h - found
> -- Looking for include file io.h
> -- Looking for include file io.h - not found
> -- Looking for include file sched.h
> -- Looking for include file sched.h - found
> -- Looking for include file regex.h
> -- Looking for include file regex.h - found
> -- Looking for posix_memalign
> -- Looking for posix_memalign - found
> -- Looking for memalign
> -- Looking for memalign - not found
> -- Looking for _aligned_malloc
> -- Looking for _aligned_malloc - not found
> -- Looking for gettimeofday
> -- Looking for gettimeofday - found
> -- Looking for sysconf
> -- Looking for sysconf - found
> -- Looking for nice
> -- Looking for nice - found
> 

Re: [gmx-users] Error in comparison of Coulomb-14 potential?

[Mark Abraham]

Hi,

That could be evidence of a bug. If you can upload your grompp inputs, tpr
and log files to a new issue on redmine.gromacs.org we can consider further.

Cheers,

Mark

On Mon, 25 Jan 2016 15:27 Andreas Mecklenfeld <
a.mecklenf...@tu-braunschweig.de> wrote:

> Dear all,
>
> I want to perform an alchemical change of state of a molecule in TIP3P,
> where I do only change the partial charges of the atomtypes. To control
> my results, I perform two MD runs with the different charge sets
> respectively.
>
> I'm interested in the Coulomb-14 interactions of the solute (since TIP3P
> has none obviously) and would have expected that the potentials of the
> end states match those of the classic runs.
>
> For the classic MD, topology A results in -5.74e+02 kJ/mol, while for B
> it's -9.04e+02 kJ/mol which seems reasonable.
> However, the Coulomb-14 potential of alchemical state A (lambda = 0) is
> -5.74e+02 kJ/mol and for state B (lambda = 1)  it's -5.69e+02 kJ/mol.
>
> I would have expected that the topology of the alchemical end state B
> matches topology B of the MD run, since all parameters should be the
> same. The results are the averages given in the log-files.
>
> Are my considerations wrong or could this be a bug in Gromacs?
>
> Thanks,
> Andreas
>
>
> --
> M. Sc. Andreas Mecklenfeld
> Stipendiat
>
> Technische Universität Braunschweig
> Institut für Thermodynamik
> Hans-Sommer-Straße 5
> 38106 Braunschweig
> Deutschland / Germany
>
> Tel: +49 (0)531 391-2634
> Fax: +49 (0)531 391-7814
>
> http://www.ift-bs.de
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Temperature Annealing

[abdus sabuj]

Hi Mark,
I have equilibrated my system very well before the production run at 300K,
but at time zero, the temperature is at 321K.

Here is the fluctuations I am getting.

time (ns)  temperature (K)
0  321
2  315
4   333
6   358
8   377
10 397

Thanks,
Sabuj

On Mon, Jan 25, 2016 at 12:38 PM, Mark Abraham 
wrote:

> Hi,
>
> What fluctuations were you seeing over the time segments?
>
> Mark
>
> On Mon, 25 Jan 2016 19:25 abdus sabuj  wrote:
>
> > Dear gmx users,
> >
> > I am trying to get viscosity as a function of temperature. So I have put
> > the following annealing inputs to the mdp file.
> >
> > ;simulated anneling
> > annealing = single
> > annealing-npoints = 6
> > annealing-time= 0 2000 4000 6000 8000 1
> > annealing-temp= 300 310 320 330 340 350
> >
> > i.e, at 10ns, the temperature should be at 350K, right? But I saw after
> my
> > npt simulation that, the last temperature reached at 400K. Why that's
> > happening, did I make any mistakes?
> >
> > Thanks,
> > Sabuj
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Build fails with AVX2_256 on Intel Xeon CPU E5-2680 v3

[Koji Tanaka]

Hi Nicolas, have you installed the latest binutils before going through the
installation? I used gcc/5.3.0, but the versions you've tried should work
fine, too.

Koji

On Mon, Jan 25, 2016 at 12:56 PM, Nicolas Cheron <
nicolas.cheron.bou...@gmail.com> wrote:

> Hi,
>
> All my installations are made from a clean build directory. I am
> using CentOS release 6.6 and the CPU is Intel Xeon CPU E5-2650 v3 @
> 2.30GHz. Here is the exact list of command that I have used (as I said, I
> have also tried with gcc4.9.3 and gcc5.2):
>
> module purge
> module load gcc/4.8.5
> cd /home2/ncheron/Programs/
> cp 00-Install/gromacs-5.1.1.tar.gz .
> tar zxf gromacs-5.1.1.tar.gz
> rm gromacs-5.1.1.tar.gz
> cd /home2/ncheron/Programs/gromacs-5.1.1
> umask 022
> mkdir build
> cd /home2/ncheron/Programs/gromacs-5.1.1/build
> mkdir /home2/ncheron/Programs/Gromacs5.1.1
>
> CMAKE_PREFIX_PATH=/home2/ncheron/Programs/LibXml_2.9.2:/home2/ncheron/Programs/Boost_1.60.0
> cmake .. -DGMX_OPENMP=ON -DGMX_THREAD_MPI=ON -DGMX_MPI=OFF -DGMX_GPU=OFF
> -DGMX_DOUBLE=OFF -DGMX_BUILD_MDRUN_ONLY=ON
> -DCMAKE_INSTALL_PREFIX=/home2/ncheron/Programs/Gromacs5.1.1
> -DGMX_BUILD_OWN_FFTW=ON
>
> -DGMX_BUILD_OWN_FFTW_URL=/home2/ncheron/Programs/00-Install/fftw-3.3.4.tar.gz
> -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_Dell -DGMX_LIBS_SUFFIX=_Dell
> -DGMX_SIMD=AVX2_256
> make -j4
> make install
>
> The error file says:
> CMake Error at cmake/gmxManageSimd.cmake:271 (message):
>   Cannot find AVX2 compiler flag.  Use a newer compiler, or choose AVX SIMD
>   (slower).
> Call Stack (most recent call first):
>   CMakeLists.txt:645 (gmx_manage_simd)
>
>
> The output file says:
> -- The C compiler identification is GNU 4.8.5
> -- The CXX compiler identification is GNU 4.8.5
> -- Check for working C compiler: /usr/local/gcc/4.8.5/bin/gcc
> -- Check for working C compiler: /usr/local/gcc/4.8.5/bin/gcc -- works
> -- Detecting C compiler ABI info
> -- Detecting C compiler ABI info - done
> -- Detecting C compile features
> -- Detecting C compile features - done
> -- Check for working CXX compiler: /usr/local/gcc/4.8.5/bin/g++
> -- Check for working CXX compiler: /usr/local/gcc/4.8.5/bin/g++ -- works
> -- Detecting CXX compiler ABI info
> -- Detecting CXX compiler ABI info - done
> -- Detecting CXX compile features
> -- Detecting CXX compile features - done
> -- Try OpenMP C flag = [-fopenmp]
> -- Performing Test OpenMP_FLAG_DETECTED
> -- Performing Test OpenMP_FLAG_DETECTED - Success
> -- Try OpenMP CXX flag = [-fopenmp]
> -- Performing Test OpenMP_FLAG_DETECTED
> -- Performing Test OpenMP_FLAG_DETECTED - Success
> -- Found OpenMP: -fopenmp
> -- Performing Test CFLAGS_WARN
> -- Performing Test CFLAGS_WARN - Success
> -- Performing Test CFLAGS_WARN_EXTRA
> -- Performing Test CFLAGS_WARN_EXTRA - Success
> -- Performing Test CFLAGS_WARN_UNDEF
> -- Performing Test CFLAGS_WARN_UNDEF - Success
> -- Performing Test CFLAGS_WARN_REL
> -- Performing Test CFLAGS_WARN_REL - Success
> -- Performing Test CFLAGS_EXCESS_PREC
> -- Performing Test CFLAGS_EXCESS_PREC - Success
> -- Performing Test CFLAGS_COPT
> -- Performing Test CFLAGS_COPT - Success
> -- Performing Test CFLAGS_NOINLINE
> -- Performing Test CFLAGS_NOINLINE - Success
> -- Performing Test CXXFLAGS_WARN
> -- Performing Test CXXFLAGS_WARN - Success
> -- Performing Test CXXFLAGS_WARN_EXTRA
> -- Performing Test CXXFLAGS_WARN_EXTRA - Success
> -- Performing Test CXXFLAGS_WARN_UNDEF
> -- Performing Test CXXFLAGS_WARN_UNDEF - Success
> -- Performing Test CXXFLAGS_WARN_REL
> -- Performing Test CXXFLAGS_WARN_REL - Success
> -- Performing Test CXXFLAGS_EXCESS_PREC
> -- Performing Test CXXFLAGS_EXCESS_PREC - Success
> -- Performing Test CXXFLAGS_COPT
> -- Performing Test CXXFLAGS_COPT - Success
> -- Performing Test CXXFLAGS_NOINLINE
> -- Performing Test CXXFLAGS_NOINLINE - Success
> -- Looking for include file unistd.h
> -- Looking for include file unistd.h - found
> -- Looking for include file pwd.h
> -- Looking for include file pwd.h - found
> -- Looking for include file dirent.h
> -- Looking for include file dirent.h - found
> -- Looking for include file time.h
> -- Looking for include file time.h - found
> -- Looking for include file sys/time.h
> -- Looking for include file sys/time.h - found
> -- Looking for include file io.h
> -- Looking for include file io.h - not found
> -- Looking for include file sched.h
> -- Looking for include file sched.h - found
> -- Looking for include file regex.h
> -- Looking for include file regex.h - found
> -- Looking for posix_memalign
> -- Looking for posix_memalign - found
> -- Looking for memalign
> -- Looking for memalign - not found
> -- Looking for _aligned_malloc
> -- Looking for _aligned_malloc - not found
> -- Looking for gettimeofday
> -- Looking for gettimeofday - found
> -- Looking for sysconf
> -- Looking for sysconf - found
> -- Looking for nice
> -- Looking for nice - found
> -- Looking for fsync
> -- Looking for fsync - found
> -- Looking for _fileno
> -- Looking for _fileno 

Re: [gmx-users] Temperature Annealing

[Justin Lemkul]

On 1/25/16 1:51 PM, abdus sabuj wrote:

Hi Mark,
I have equilibrated my system very well before the production run at 300K,
but at time zero, the temperature is at 321K.

Here is the fluctuations I am getting.

time (ns)  temperature (K)
0  321
2  315
4   333
6   358
8   377
10 397



Please provide the full .mdp file, rather than just the few lines you think are 
important, as well as the commands used to continue from the previous run.  You 
probably have other incorrect settings and/or are continuing the run wrong. 
Time zero should match the previous state; the fact that it doesn't suggests 
you're not doing what you think you're doing.


-Justin


Thanks,
Sabuj

On Mon, Jan 25, 2016 at 12:38 PM, Mark Abraham 
wrote:


Hi,

What fluctuations were you seeing over the time segments?

Mark

On Mon, 25 Jan 2016 19:25 abdus sabuj  wrote:


Dear gmx users,

I am trying to get viscosity as a function of temperature. So I have put
the following annealing inputs to the mdp file.

;simulated anneling
annealing = single
annealing-npoints = 6
annealing-time= 0 2000 4000 6000 8000 1
annealing-temp= 300 310 320 330 340 350

i.e, at 10ns, the temperature should be at 350K, right? But I saw after

my

npt simulation that, the last temperature reached at 400K. Why that's
happening, did I make any mistakes?

Thanks,
Sabuj
--
Gromacs Users mailing list

* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.


--
Gromacs Users mailing list

* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Temperature Annealing

[Mark Abraham]

Hi,

What fluctuations were you seeing over the time segments?

Mark

On Mon, 25 Jan 2016 19:25 abdus sabuj  wrote:

> Dear gmx users,
>
> I am trying to get viscosity as a function of temperature. So I have put
> the following annealing inputs to the mdp file.
>
> ;simulated anneling
> annealing = single
> annealing-npoints = 6
> annealing-time= 0 2000 4000 6000 8000 1
> annealing-temp= 300 310 320 330 340 350
>
> i.e, at 10ns, the temperature should be at 350K, right? But I saw after my
> npt simulation that, the last temperature reached at 400K. Why that's
> happening, did I make any mistakes?
>
> Thanks,
> Sabuj
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Temperature Annealing

[abdus sabuj]

Hi Justin,

I have used these following commands in npt and final .tpr production.

grompp -f npt.mdp -p topol.top -c nvt.gro -o npt.tpr


grompp -f final.mdp -p topol.top -c npt.gro -o final.tpr

Thanks,
Sabuj


On Mon, Jan 25, 2016 at 1:55 PM, Justin Lemkul  wrote:

>
>
> On 1/25/16 2:41 PM, abdus sabuj wrote:
>
>> Hi Justin,
>>
>> Here is the mdp file I used for NPT equilibration...
>>
>>
>> integrator   = md
>> nsteps   = 1000
>> dt   = 0.001
>> nstenergy= 1000
>> nstxout  = 1000
>> nstvout  = 1000
>>
>>
>>
>>
>>
>> vdw-type = cut-off
>>
>>
>> continuation= yes; first dynamics run
>> constraint_algorithm = lincs; holonomic constraints
>> constraints = all-bonds ; all bonds (even heavy atom-H
>> bonds) constrained
>> ;lincs_iter  = 1 ; accuracy of LINCS
>> ;lincs_order = 4 ; also related to accuracy
>> lincs-warnangle = 90; warning after rotating the bond
>>
>>
>> ns_type = grid  ; search neighboring grid cels
>> nstlist = 10 ; 10 fs
>> rlist   = 1.4   ; short-range neighborlist cutoff (in nm)
>> rcoulomb= 1.4   ; short-range electrostatic cutoff (in nm)
>> rvdw= 1.4   ; short-range van der Waals cutoff (in nm)
>> coulombtype = PME   ; Particle Mesh Ewald for long-range
>> electrostatics
>> pme_order   = 4 ; cubic interpolation
>> fourierspacing  = 0.16  ; grid spacing for FFT
>>
>> ; set temperature to 300K
>> tcoupl   = v-rescale
>> tc-grps  = system
>> tau-t= 0.1
>> ref-t= 300
>> ; and pressure to 1 bar
>> pcoupl   = berendsen
>> ref-p= 1
>> compressibility  = 4.5e-5
>> tau-p= 5
>> ; generate initial velocities
>> gen-vel  = no
>> ;gen-temp = 300
>> ;gen_seed= -1
>> ; Periodic boundary conditions
>> pbc = xyz   ; 3-D PBC
>> ; Dispersion correction
>> DispCorr= EnerPres  ; account for cut-off vdW scheme
>>
>> ; COM motion removal
>> ; These options remove motion of the protein/bilayer relative to the
>> solvent/ions
>> nstcomm = 1
>> comm-mode   = Linear
>> comm-grps   = system
>>
>>
>> ...
>>
>>
>> And for Production run, I am using the mdp file as below
>>
>>
>> integrator   = md
>> nsteps   =1000
>> dt   = 0.001
>> nstenergy= 1000
>> nstxout  = 1000
>> nstvout  = 1000
>>
>>
>> vdw-type = cut-off
>>
>> continuation= yes; first dynamics run
>> constraint_algorithm = lincs; holonomic constraints
>> constraints = all-bonds ; all bonds (even heavy atom-H
>> bonds) constrained
>> ;lincs_iter  = 1 ; accuracy of LINCS
>> ;lincs_order = 8 ; also related to accuracy
>> lincs-warnangle = 90; warning after rotating the bond
>>
>>
>> ns_type = grid  ; search neighboring grid cels
>> nstlist = 10 ; 10 fs
>> rlist   = 1.4   ; short-range neighborlist cutoff (in nm)
>> rcoulomb= 1.4   ; short-range electrostatic cutoff (in nm)
>> rvdw= 1.4   ; short-range van der Waals cutoff (in nm)
>>
>> coulombtype =PME   ; Particle Mesh Ewald for long-range
>> electrostatics
>> pme_order   = 4 ; cubic interpolation
>> fourierspacing  = 0.16  ; grid spacing for FFT
>>
>> ; set temperature to 300K
>> tcoupl   = Nose-Hoover
>> tc-grps  = system
>> tau-t= 0.2
>> ref-t= 300
>> ; and pressure to 1 bar
>> pcoupl   = Parrinello-Rahman
>> ref-p= 1
>> compressibility  = 4.5e-5
>> tau-p= 5
>> pcoupltype  = isotropic
>> ; generate initial velocities
>> gen-vel  = no
>> ;gen-temp = 300
>> ;gen_seed= -1
>> ; Periodic boundary conditions
>> pbc = xyz   ; 3-D PBC
>> ; Dispersion correction
>> DispCorr= EnerPres ; account for cut-off vdW scheme
>>
>> ;simulated anneling
>> annealing = single
>> annealing-npoints = 6
>> annealing-time= 0 2000 4000 6000 8000 1
>> annealing-temp= 300 310 320 330 340 350
>>
>> ; COM motion removal
>> ; These options remove motion of the protein/bilayer relative to the
>> solvent/ions
>> nstcomm 

Re: [gmx-users] GPU efficiency

[Szilárd Páll]

Hi Albert,

I have to concur with Mark's point, it's not hard at all to pick (or
happen to benchmark) circumstances under which one code is
significantly faster than the other.

In order to understand the differences, please share:
- GROMACS logs
[ - full hardware & software specs, compilers, CUDA, etc (will be in
the GROMACS log ;) ]
- full set of AMBER and Desmond setting and algorithms used - there
may be considerable differences in the algorithmic choices that favor
one software or the other.

These details will probably confirm what Mark hinted: a CPU-bound run
will be unfavorable to GROMACS. Depending on the hardware balance
you'll find that mdrun can be slower or faster than AMBER (with
equivalent algorithms). I know because I've compared ;)

On Sun, Jan 24, 2016 at 4:43 PM, Albert  wrote:
> Dear Mark:
>
> Thanks for the comments.
>
> I am also very surprised to see the results.  In my impression, Gromacs
> always has the best efficiency for MD GPU running
>
> I talked this with one of my friends who also uses Gromacs for several
> years. And he told me that he also found similar testing results by himself
> recentlyIt would be even worse that Gromacs heavily use both CPU+GPU and
> the efficiency is obviously much slower than Amber.

I'm not sure I follow you, but I'm afraid that conclusion could be
incorrect! Could you please clarify what you mean?

One could easily pick a hardware setup that would for instance show
that AMBER-GPU performs worse or some other hardware on which
AMBER-GPU is faster than GROMACS. If you're simply comparing on the
hardware you have (and have made sure to do the correct comparison),
of course, it's going to be the relevant conclusion *for your case*,
but that conclusion does not generalize easily!

> What's need to point out is that Desmond even uses 1 GPU+1 CPU, the speed is
> as fast as Amber running with 2 GPU+2CPU. I contacted Desmond supporters,
> and they told me that they optimize the algorithm recently which fasten the
> running 2 times comparing with previous Desmond release.  As we all known
> that Desmond developer created ANTON which is amazing. It seems that they
> have some breakthrough in GPU these days although currently it only supports
> 1GPU+1CPU for a single job. If in the near future, they somehow manage to
> use multiple GPU for a single job, it will change everything a lot.

Is it multiple time-stepping that they were referring to? AFAIK
Desmond typically uses 2.5 fs time-step and PME every second step. For
a fair comparison you should employ algorithms that accelerate
sampling in the other codes too: virtual sites in GROMACS (up to 2.5x
throughput) and HMR in AMBER (up to 2x throughput). If you did not use
these features, factoring these in will immediately result in much
closer performance numbers.

If there is something else the the Desmond devs came up with, I'd be
curious to hear about it, but the very sparse public information
showed (last time I checked a 1-2 months ago) no performance advantage
wrt. GROMACS.

Cheers,
--
Szilárd

> regards
>
> Albert
>
> On 01/24/2016 09:54 AM, Mark Abraham wrote:
>>
>> Hi,
>>
>> You need to use the hidden -fasterthanamber mdrun benchmarking option!;-)
>> Comparing GROMACS with AMBER on the same hardware is always unfair to one
>> of them, because we use the CPU heavily and they do not. Otherwise we
>> can't
>> comment until we've seen log files shared e.g. on a file sharing service.
>> List won't take attachments.
>>
>> Mark
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
> mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Brefeldin A and GDP parameters

[Jeremy T First]

Hello all,

Has anyone parameterized Brefeldin A or GDP for Amber force fields? I wish
to simulate a protein with BFA and GDP as ligands, but have so far been
unable to find parameters for these molecules.

I have a procedure to do so using RED and Gamess, but understand this is a
difficult process and would prefer to use parameters already out there if
they exist.


Best,

Jeremy
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 141, Issue 106

[lloyd riggs]

Dear Sabuj,

 

It would be difficult to help without more info (size of system, contents of system, .mdp file, etc...).  I have not used simulated annealing in years, and when I used the software in the past, it was mostly structure determination from unknown phases (cooling an unknown partial structure from say 450 to 290 and running molreplacement every 10 degrees with several annealed structures, or taking structures from 10 seperate runs for the same thng)...

 

If the system (yours) however is 50 degrees over/under or fluctuating this much, it would indicate your equilibrium was not long enough, probably between temperature changes.  You could try increasing time segments to 5-20 ns between temperature changes, or run a simple eq, then extended sims for 10-50 ns as seperate runs at a set temperature.  As I assume a gaussian distribution, you might have to do multiple runs in either experimental set up, say 3-4 at each temperature, to generate the data with the natural gaussian distribution for kinetics (viscosity, density, etc...).

 

Good luck,

 

Stephan Watkins, PhD

 
 

Message: 6
Date: Mon, 25 Jan 2016 18:38:34 +
From: Mark Abraham 
To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Temperature Annealing
Message-ID:

[gmx-users] How to get an index file containing non polar atoms in gromacs?

[Shima ebrahimi]

 

Dear Users, 

I want to determine hydrophobic interaction between ligand and protein
using g_mindist. However, how can I identify non-polar atoms and specify
them in the index file.Could anyone help me? 
Regards, 
Shima 
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] g_correlation

[Felix W.-H. Weng]

Dear all:

I'm using the generalized correlation analysis tool developed by Lange and
Grubmüller. Does anyone know the option for setting the range of
correlation values? Say, 0 to 1?

Any advice would be appreciated, thanks in advance.

Best,
Wei-Hsiang
--
Wei-Hsiang Weng (翁偉翔)
Department of Life Sciences
Tzu-Chi University
No.701, Sec. 3, Zhongyang Rd. Hualien 97004, Taiwan
Tel.: +886-975-232-245
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.